


Difficult Choices

by reeby10



Category: Stargate Atlantis
Genre: Alternate Universe - Canon Divergence, Gen, Independent Atlantis, breaking away from Earth
Language: English
Status: Completed
Published: 2017-04-24
Updated: 2017-04-24
Packaged: 2018-10-23 08:51:26
Rating: General Audiences
Warnings: No Archive Warnings Apply
Chapters: 1
Words: 2,315
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/10716168
Author URL: https://archiveofourown.org/users/reeby10/pseuds/reeby10
Summary: Earth isn't taking the Wraith threat seriously, so Atlantis has to decide what they'll do about.





	Difficult Choices

**Author's Note:**

  * For [badger79](https://archiveofourown.org/users/badger79/gifts).



> Space Swap gift for badger79. I hope you like it!
> 
> This diverges from canon fairly early in s1, basically just after the Daedalus arrives and disregarding pretty much everything else that happens around then lol I really just wanted to explore how they would go about breaking away from Earth so early in the series, since I feel like most other independent Atlantis fics take place much later.

John still didn’t understand how no one on Earth could see how serious the situation was. How dangerous the Wraith were both to the Pegasus galaxy and to Earth itself. He’d thought that the weeks of debriefs with Colonel Caldwell and the IOA rep after what happened with Sumner would tell them that much at least. He’d thought at the very least that they’d replace him and put someone more suitable in charge.

But they hadn’t. Apparently the IOA had decided that with all the other threats closer to home, the ones in Pegasus didn’t deserve their attention. That hadn’t exactly gone over well with most of the expedition.

Anyone could see how tensions started to rise as Earth continued to refuse to send more men or supplies. Atlantis wasn’t exactly struggling yet, but they could all see it coming up quickly. Fighting the Wraith took a lot of resources and a lot of manpower, something they couldn’t risk too much of if they weren’t going to be able to get help from Earth. They were conserving as much as they could, but everyone was afraid that soon wouldn’t be enough.

All the senior staff and ranking members of the military were meeting to discuss just that. The heads of all the departments had been asked a week before to prepare predictions based on remaining supplies and the current outlook. Sitting at the table, looking around at all the grim faces, John was pretty sure the future wasn’t looking so good.

“Alright, everyone, settle down please,” Elizabeth called, eyeing those few still talking, like Rodney, until they quieted.

“Thank you,” she said. She smiled, a movement John thought was more out of ingrained politeness than anything else. “As you all know, we’re meeting today to discuss the future of this expedition. Earth, that is SGC and the IOA, have.. not been very supportive of the unique difficulties we are facing with the Wraith. They have refused most of our requests for more personnel and resources on the grounds that it is more important to protect the Earth and the Milky Way.

“Myself and Major Sheppard have looked over all of your reports,” she continued. “They’ve been compiled into a document that all of you can access on the Atlantis intranet. Please feel free to follow along there as we hear brief reports from each department head.”

There was a moment of intense movement as everyone got out laptops and searched for the document, though John just sat back and watched, as did Teyla and Rodney on either side of him. He was sure both of them had read the reports already. Though to be fair, Rodney might just not care enough about the other departments, particularly the soft sciences, to to give it a look.

It was difficult for John not to doze off as each department head stood and gave a brief summary of their report, including personnel and resource needs in the immediate future. He knew it was important--heck, this had been partly his idea in the first place--but he got bored easily, and hearing the botanists talk about crop growth wasn’t exactly stimulating for him. As such, he tried to keep the hangman game he had going with Rodney as inconspicuous as possible.

It took almost two hours to get through everyone, though it felt like much longer. None of the reports were good, everyone suffering the effects of being understaffed and undersupplied. By the end, John could see how shaken many of the scientists, and even a few of his own men, were by what they’d heard. Even Elizabeth, who’d read all the reports beforehand, was looking grim.

The big problem as John saw it was that Earth didn’t see Atlantis as a viable _military_ base in the various fights going on in the Milky Way. And because of that, they didn’t see the Atlantis expedition as particularly important anymore, and thus not worth expending more resources on. Military wasn’t what they’d come here for in the first place, but it was apparently what had become most important since they’d left.

John wasn’t sure what they could do about that. He and Elizabeth had met the day before, talking late into the night without coming up with many solutions, at least none that Elizabeth hadn’t deemed too extreme to immediately pursue. John was beginning to think that extreme might be the only way they were going to survive out here without Earth’s help.

“Thank you for your reports,” Elizabeth finally said, interrupting the murmured conversations that had started up all over the room. “As you can see, the situation is going to become rather untenable very quickly unless we do something. So that’s why we’re here today, to figure out what to do.”

Everyone started talking at once, words tumbling over each other until it was impossible to separate one person’s speech from another. Every once in a while, John could hear snatches of scared or angry conversation, not enough to really get a feel for what the overarching thought on the matter was. Elizabeth let it go on for a few minutes, maybe hoping they’d exhaust themselves or talk themselves around to a good idea. When she cleared her throat, though, they barely quieted. She frowned and John stood, chair scraping back on the floor.

“Hey,” he said, pitching his voice to carry over the crowd. His men silenced immediately, but it took a glare from Rodney for a few of the more loquacious scientists to shut up. “We don’t have time for not paying attention, so pay attention.”

Elizabeth nodded her thanks. “I know many of you are scared or angry about this,” she said slowly, unease clear on her face. John felt the same, though he tried to keep from showing it. “I am too. But we need to come up with ideas on what to do if we’re going to survive out here.”

“There are a few different scenarios we’ve already discussed,” John continued, knowing how uncomfortable Elizabeth was with some of the choices but knowing the others still needed to hear them. “Are we going to wait it out and hope SGC eventually deigns to send us more supplies? Are we going to return to Earth and call the expedition a wash? Are we going to separate entirely and try to raise our own resources here in Pegasus?”

A murmur of unease swept the room, something so palpable John could almost feel it. This was not an easy choice, not for any of them.

Almost all of the people here were from Earth and though they’d not expected to ever return there at the beginning of the expedition, it was still their homeworld. There was still loyalty there, even if the loyalty wasn’t be rewarded or acknowledged at the moment. To some of them, returning might sound like a good idea. To some of them, separating might seem like an impossibility.

“Please remember that we do not all have to make to make the same choice either,” Elizabeth said over the growing noise. “If we decide to stay and wait or… or separate, you can still go back to Earth if that’s what you’d wish.”

Out of the corner of his eye, John could see Rodney frowning. He was fairly sure Rodney would stay no matter what, Atlantis and the Pegasus galaxy was where he belonged. On John’s other side, Teyla sat with an entirely serene expression on her face. She would stay of course, she was a Pegasus native, but John wondered how much she and her people would be willing to help Atlantis if it came to them separating from Earth entirely. He knew from experience that there were friends and then there were _friends_.

As if she could sense him looking at her, Teyla smiled and leaned close enough that he was the only one who would be able to hear her. “I know this will be difficult for your people,” she said. “But know that I will do all I can to help you. And I know my people feel the same.”

John nodded, relief relaxing the ever present tension in his muscles just a little. Sometimes he wondered a little uneasily if she could read his mind, but in this instance he was glad. “Thanks.”

“I know this will take a lot of thinking and a lot of talking to figure out,” Elizabeth said loudly, drawing John’s and many other’s attention back to her. “Please be sure to share the information discussed today with the rest of your departments. I think the best option for now is to take a vote on what the expedition as a whole will do. This will take place Friday and will be mandatory for all expedition members.”

There were nods from around the room and she smiled a little. “Good. If you or your people have any questions or concerns between now and then, please see myself or Major Sheppard,” she continued, locking eyes with John and receiving a nod from him as well. “Dismissed.”

***

Friday was rife with tension from the moment John woke up. People were coming up to him as soon as he got to the mess, asking about the upcoming vote and his thoughts on what they should do. He tried to be vague and point them in the direction of their department heads, but even that was thoroughly exhausting. Not for the first time, he thought about how he was afraid he really wasn’t up for the task of being half the leadership of the expedition.

Thankfully the vote was set to take place in the four hours around lunch, so he didn’t have to try to avoid everyone for too long. He spent the time in his office, which he usually hated, but it was hidden enough that few people other than Teyla or Bates was likely to find him there.

Teyla was the one that found him there, staring moodily at the wall as he avoided doing any of the paperwork he probably should be doing. He’d expected a call on the radio when the vote was over, but he followed along easily enough as she led the way to Elizabeth’s office. Rodney, Bates, and several of the other department heads were there already.

“So?” he asked, taking his place with the rest. “What’s the verdict?”

Elizabeth gave a strained smile, turning the laptop on her desk to face them. “Overwhelmingly, the vote was to break off from Earth.”

John let out a breath he hadn’t even realized he’d been holding. This was good. This was what he’d been hoping for. And apparently what pretty much everyone else in the expedition had been hoping for, going by the results he saw on the screen. They were going to cut themselves off from Earth.

“What now?” Rodney asked, sounding far more excited than the situation probably warranted. But then again, he’d made no secret over the past week of where he thought the SGC and IOA could stick their refusal of resources.

“We have made _some_ plans for this so far,” Elizabeth said, clicking through a few screens on her laptop. “I would, however, like to have all the department heads submit plans for what they can provide for the expedition, what they will need going forward, and any ideas for getting us to a stable point without Earth.”

John nodded along with the others, mind already making a list for the military contingency. Guns and ammo would become a problem before too long, and uniforms sometime in the future. He was sure Bates, as much as he disliked the man, would have something more comprehensive prepared in the next couple of days.

“What about those who do not wish to leave Earth?” Teyla asked.

“We will, of course, give them the option to return once we have formalized the secession,” Elizabeth said with a heavy sigh. “It will take time to get everything together and decide how Atlantis will be run without Earth making the rules. They will have plenty of chances to decide if they want to go.”

The silence became a little more solemn after that, the reality of this decision finally sinking in. John hoped that not too many people would choose to return, they couldn’t afford to lose many more people without having to make some serious changes. Though he supposed they were going to have to do that anyway, for good or for bad. Without Earth making their decisions for them, they were going to have to figure everything out on their own.

The group broke up a few minutes later, everyone going to inform their departments of the results of the vote. There would probably be a party later, and John hoped Radek would bring out some of his homemade moonshine. He thought that after today, they all needed a little of that.

John hung back, waving for Teyla and Rodney to leave without him, and walked up to Elizabeth’s desk. She looked exhausted and he suddenly felt for her having to organize all of this. She’d been prepared for being the leader of the expedition, but he didn’t think even she had been prepared for the realities of Atlantis.

“How do you feel about this?”

She shrugged, but John could see the tension she still held. Despite everything the SGC and IOA had said and done, or rather not done, he was pretty sure she hadn’t exactly been excited about cutting off contract with Earth. She was still too attached, not that he could really blame her for that.

“It is what it is,” she said, and he could only nod. They’d learned that pretty quickly out here. “It was a difficult choice for all of us, now we just have to figure out how to live with it.”

**Author's Note:**

> Concrit welcome. If you like my fic, feel free to come hit me up [on tumblr](http://voldiebuns.tumblr.com/)!


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